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  1. Replicable brain–phenotype associations require large-scale neuroimaging data

    Numerous neuroimaging studies have investigated the neural basis of interindividual differences but the replicability of brain–phenotype associations...

    Shu Liu, Abdel Abdellaoui, ... Guido A. van Wingen in Nature Human Behaviour
    Article 26 June 2023
  2. Towards genetic improvement of social behaviours in livestock using large-scale sensor data: data simulation and genetic analysis

    Background

    Harmful social behaviours, such as injurious feather pecking in poultry and tail biting in swine, reduce animal welfare and production...

    Zhuoshi Wang, Harmen Doekes, Piter Bijma in Genetics Selection Evolution
    Article Open access 28 September 2023
  3. rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data

    Pre-mRNA alternative splicing is a prevalent mechanism for diversifying eukaryotic transcriptomes and proteomes. Regulated alternative splicing plays...

    Yuanyuan Wang, Zhijie **e, ... Yi **ng in Nature Protocols
    Article 23 February 2024
  4. An MSstats workflow for detecting differentially abundant proteins in large-scale data-independent acquisition mass spectrometry experiments with FragPipe processing

    Technological advances in mass spectrometry and proteomics have made it possible to perform larger-scale and more-complex experiments. The volume and...

    Devon Kohler, Mateusz Staniak, ... Olga Vitek in Nature Protocols
    Article 20 May 2024
  5. Gapr for large-scale collaborative single-neuron reconstruction

    Whole-brain analysis of single-neuron morphology is crucial for unraveling the complex structure of the brain. However, large-scale neuron...

    Lingfeng Gou, Yanzhi Wang, ... Jun Yan in Nature Methods
    Article 03 July 2024
  6. Large-scale foundation model on single-cell transcriptomics

    Large pretrained models have become foundation models leading to breakthroughs in natural language processing and related fields. Develo**...

    Minsheng Hao, **g Gong, ... Le Song in Nature Methods
    Article 06 June 2024
  7. Comparing models of learning and relearning in large-scale cognitive training data sets

    Practice in real-world settings exhibits many idiosyncracies of scheduling and duration that can only be roughly approximated by laboratory research....

    Aakriti Kumar, Aaron S. Benjamin, ... Mark Steyvers in npj Science of Learning
    Article Open access 04 October 2022
  8. MetHoS: a platform for large-scale processing, storage and analysis of metabolomics data

    Background

    Modern mass spectrometry has revolutionized the detection and analysis of metabolites but likewise, let the data skyrocket with...

    Konstantinos Tzanakis, Tim W. Nattkemper, ... Stefan P. Albaum in BMC Bioinformatics
    Article Open access 08 July 2022
  9. Elucidating disease-associated mechanisms triggered by pollutants via the epigenetic landscape using large-scale ChIP-Seq data

    Background

    Despite well-documented effects on human health, the action modes of environmental pollutants are incompletely understood. Although...

    Zhaonan Zou, Yuka Yoshimura, ... Shinya Oki in Epigenetics & Chromatin
    Article Open access 25 September 2023
  10. Large-scale behavioural data are key to climate policy

    Mirjam A. Jenny, Cornelia Betsch in Nature Human Behaviour
    Article 16 November 2022
  11. Effect of sample size on the estimation of forest inventory attributes using airborne LiDAR data in large-scale subtropical areas

    Key message

    Sample size (number of plots) may significantly affect the accuracy of forest attribute estimations using airborne LiDAR data in...

    Chungan Li, Zhu Yu, ... Mei Zhou in Annals of Forest Science
    Article Open access 20 October 2023
  12. Removing unwanted variation from large-scale RNA sequencing data with PRPS

    Accurate identification and effective removal of unwanted variation is essential to derive meaningful biological results from RNA sequencing...

    Ramyar Molania, Momeneh Foroutan, ... Terence P. Speed in Nature Biotechnology
    Article Open access 15 September 2022
  13. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data

    Julianus Pfeuffer, Chris Bielow, ... Timo Sachsenberg in Nature Methods
    Article 16 February 2024
  14. An assessment of long-term and large-scale wetlands change dynamics in the Limpopo transboundary river basin using cloud-based Earth observation data

    Significant progress has been made in monitoring and assessing the effects of land use and land cover (LULC) changes on wetland extent. However, our...

    Siyamthanda Gxokwe, Timothy Dube, Dominic Mazvimavi in Wetlands Ecology and Management
    Article Open access 30 November 2023
  15. easyMF: A Web Platform for Matrix Factorization-Based Gene Discovery from Large-scale Transcriptome Data

    With the development of high-throughput experimental technologies, large-scale RNA sequencing (RNA-Seq) data have been and continue to be produced,...

    Wenlong Ma, Siyuan Chen, ... Chuang Ma in Interdisciplinary Sciences: Computational Life Sciences
    Article 18 May 2022
  16. The theory on and software simulating large-scale genomic data for genotype-by-environment interactions

    Background

    With the emphasis on analysing genotype-by-environment interactions within the framework of genomic selection and genome-wide association...

    **u** Li, Hailiang Song, ... **angdong Ding in BMC Genomics
    Article Open access 05 December 2021
  17. Large-scale citizen science reveals predictors of sensorimotor adaptation

    Sensorimotor adaptation is essential for kee** our movements well calibrated in response to changes in the body and environment. For over a...

    Jonathan S. Tsay, Hrach Asmerian, ... Ken Nakayama in Nature Human Behaviour
    Article 30 January 2024
  18. A resource database for protein kinase substrate sequence-preference motifs based on large-scale mass spectrometry data

    Background

    Protein phosphorylation is one of the most prevalent posttranslational modifications involved in molecular control of cellular processes,...

    Brian G. Poll, Kirby T. Leo, ... Mark A. Knepper in Cell Communication and Signaling
    Article Open access 19 February 2024
  19. High-resolution structural variants catalogue in a large-scale whole genome sequenced bovine family cohort data

    Background

    Structural variants (SVs) are chromosomal segments that differ between genomes, such as deletions, duplications, insertions, inversions and...

    Young-Lim Lee, Mirte Bosse, ... Carole Charlier in BMC Genomics
    Article Open access 01 May 2023
  20. Using pre-selected variants from large-scale whole-genome sequence data for single-step genomic predictions in pigs

    Background

    Whole-genome sequence (WGS) data harbor causative variants that may not be present in standard single nucleotide polymorphism (SNP) chip...

    Sungbong Jang, Roger Ros-Freixedes, ... Daniela Lourenco in Genetics Selection Evolution
    Article Open access 26 July 2023
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